mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999999923898413 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:140230370A>CN/A show variant in all transcripts IGV

HGNC symbol

PCDHA5

Ensembl transcript ID

ENST00000529859

Genbank transcript ID

NM_018908

UniProt peptide

Q9Y5H7

alteration type

single base exchange

alteration region

intron

DNA changes

g.29149A>C

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

Reference ID: rs369636

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1070	996	2066
ExAC	25467	-18167	7300

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.74	0.001
	-0.673	0
(flanking)	-0.021	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	29150	wt: 0.8948 / mu: 0.9022 (marginal change - not scored)	wt: GGGTAAGCAGAAGAC mu: GGGTCAGCAGAAGAC	GTAA\|gcag
Donor increased	29153	wt: 0.26 / mu: 0.56	wt: TAAGCAGAAGACCGA mu: TCAGCAGAAGACCGA	AGCA\|gaag
Donor increased	29140	wt: 0.52 / mu: 0.77	wt: GCTCTGGCGAGGGTA mu: GCTCTGGCGAGGGTC	TCTG\|gcga

distance from splice site

26658

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
718	936	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
773	890	REGION	5 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
785	788	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
818	821	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
877	890	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
909	916	COMPBIAS	Poly-Lys.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

position (AA) of stopcodon in wt / mu AA sequence

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

1 / 1

chromosome

strand

last intron/exon boundary

2501

theoretical NMD boundary in CDS

2450

length of CDS

2811

coding sequence (CDS) position

N/A

cDNA position
(for ins/del: last normal base / first normal base)

N/A

gDNA position
(for ins/del: last normal base / first normal base)

29149

chromosomal position
(for ins/del: last normal base / first normal base)

140230370

original gDNA sequence snippet

GGGTGTGCTCTGGCGAGGGTAAGCAGAAGACCGACCTCATG

altered gDNA sequence snippet

GGGTGTGCTCTGGCGAGGGTCAGCAGAAGACCGACCTCATG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVYSRRGSLG SRLLLLWLLL AYWKAGSGQL HYSIPEEAKH GTFVGRIAQD LGLELAELVP
RLFRVASKGR GDLLEVNLQN GILFVNSRID REELCRRRAE CSIHLEVIVD RPLQVFHVEV
AVKDINDNPP RFSRQEQRLF ILESRMPDSR FPLEGASDLD IGANAQLRYR LNPNEYFDLD
VKTNEEETNF LELVLRKSLD REETQEHRLL VIATDGGKPE LTGTVQLLIN VLDANDNAPE
FDKSIYNVRL LENAPSGTLV IKLNASDADE GINKEIVYFF SNLVLDDVKS KFIINSNTGE
IKVNGELDYE DYNSYEINID AMDKSTFPLS GHCKVVVKLL DVNDNTPEMA ITTLFLPVKE
DAPLSTVIAL ISVSDRDSGA NGQVTCSLMP HVPFKLVSTF KNYYSLVLDS ALDRESVSVY
ELVVTARDGG SPSLWATASV SVEVADVNDN APAFAQPQYT VFVKENNPPG CHIFTVSARD
ADAQENALVS YSLVERRVGE RPLSSYVSVH AESGKVYALQ PLDHEEVELL QFQVSARDAG
VPPLGSNVTL QVFVLDENDN APALLVPRVG GTGGAVSELV PRSVGAGHVV AKVRAVDPDS
GYNAWLSYEL QPAPGSARIP FRVGLYTGEI STTRSLDETE APRHRLLVLV KDHGEPPLTA
TATVLVSLVE SGQAPKASSR ASAGAVGPEA ALVDVNVYLI IAICAVSSLL VLTLLLYTAL
RCSAQPTEAV CTRGKPTLLC SSAVGSWSYS QQRRQRVCSG EAPPKTDLMA FSPSLPQGPT
STDNPRQPNP DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV
SPPVGAGVNS NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI
TFGKKEETKK KKKKKKGNKT QEKKEKGNST TDNSDQ*

mutated AA sequence

N/A

speed

0.81 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project